IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v16y2025i1d10.1038_s41467-025-62641-w.html
   My bibliography  Save this article

Lactuca super-pangenome provides insights into lettuce genome evolution and domestication

Author

Listed:
  • Shuai Cao

    (National University of Singapore)

  • Nunchanoke Sawettalake

    (National University of Singapore)

  • Lisha Shen

    (National University of Singapore
    National University of Singapore)

Abstract

Lettuce (Lactuca sativa L.) is among the most widely cultivated and consumed vegetables globally, valued for its phytonutrients beneficial for human health. Here, we report the high-quality reference super-pangenome for the Lactuca genus by integrating 12 chromosome-scale genomes from representative cultivated lettuce morphotypes, landrace, and wild relatives, and investigate lettuce genome evolution and domestication. These assemblies exhibit diverse genome sizes ranging from 2.1 Gb to 5.5 Gb with abundant repetitive sequences, and expansion of repetitive sequences, associated with low DNA methylation levels, likely contributes to the genome size variations. Furthermore, by constructing a graph-based lettuce pangenome reference, we explore the landscape, genomic, and epigenetic features of structural variations, and reveal their contributions to gene expression and domestication. We also identify copy number variations in FLOWERING LOCUS C in association with delayed flowering in cultivated lettuce. Overall, this comprehensive Lactuca super-pangenome assembly will expedite functional genomics studies and breeding efforts of this globally important crop.

Suggested Citation

  • Shuai Cao & Nunchanoke Sawettalake & Lisha Shen, 2025. "Lactuca super-pangenome provides insights into lettuce genome evolution and domestication," Nature Communications, Nature, vol. 16(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-62641-w
    DOI: 10.1038/s41467-025-62641-w
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-025-62641-w
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-025-62641-w?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Lin Zhang & Hong Yu & Bin Ma & Guifu Liu & Jianjun Wang & Junmin Wang & Rongcun Gao & Jinjun Li & Jiyun Liu & Jing Xu & Yingying Zhang & Qun Li & Xuehui Huang & Jianlong Xu & Jianming Li & Qian Qian &, 2017. "A natural tandem array alleviates epigenetic repression of IPA1 and leads to superior yielding rice," Nature Communications, Nature, vol. 8(1), pages 1-10, April.
    2. Sebastian Reyes-Chin-Wo & Zhiwen Wang & Xinhua Yang & Alexander Kozik & Siwaret Arikit & Chi Song & Liangfeng Xia & Lutz Froenicke & Dean O. Lavelle & María-José Truco & Rui Xia & Shilin Zhu & Chunyan, 2017. "Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce," Nature Communications, Nature, vol. 8(1), pages 1-11, April.
    3. Lei Zhang & Wenqing Su & Rong Tao & Weiyi Zhang & Jiongjiong Chen & Peiyao Wu & Chenghuan Yan & Yue Jia & Robert M. Larkin & Dean Lavelle & Maria-Jose Truco & Sebastian Reyes Chin-Wo & Richard W. Mich, 2017. "RNA sequencing provides insights into the evolution of lettuce and the regulation of flavonoid biosynthesis," Nature Communications, Nature, vol. 8(1), pages 1-12, December.
    4. Gen Xu & Jing Lyu & Qing Li & Han Liu & Dafang Wang & Mei Zhang & Nathan M. Springer & Jeffrey Ross-Ibarra & Jinliang Yang, 2020. "Evolutionary and functional genomics of DNA methylation in maize domestication and improvement," Nature Communications, Nature, vol. 11(1), pages 1-12, December.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Zhen-Hui Wang & Xin-Feng Wang & Tianyuan Lu & Ming-Rui Li & Peng Jiang & Jing Zhao & Si-Tong Liu & Xue-Qi Fu & Jonathan F. Wendel & Yves Peer & Bao Liu & Lin-Feng Li, 2022. "Reshuffling of the ancestral core-eudicot genome shaped chromatin topology and epigenetic modification in Panax," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    2. Tao Zhu & Chunjiao Xia & Ranran Yu & Xinkai Zhou & Xingbing Xu & Lin Wang & Zhanxiang Zong & Junjiao Yang & Yinmeng Liu & Luchang Ming & Yuxin You & Dijun Chen & Weibo Xie, 2024. "Comprehensive mapping and modelling of the rice regulome landscape unveils the regulatory architecture underlying complex traits," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    3. Fuxi Rong & Yusong Lv & Pingchuan Deng & Xia Wu & Yaqi Zhang & Erkui Yue & Yuxin Shen & Sajid Muhammad & Fangrui Ni & Hongwu Bian & Xiangjin Wei & Weijun Zhou & Peisong Hu & Liang Wu, 2024. "Switching action modes of miR408-5p mediates auxin signaling in rice," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    4. Huiying He & Yue Leng & Xinglan Cao & Yiwang Zhu & Xiaoxia Li & Qiaoling Yuan & Bin Zhang & Wenchuang He & Hua Wei & Xiangpei Liu & Qiang Xu & Mingliang Guo & Hong Zhang & Longbo Yang & Yang Lv & Xian, 2024. "The pan-tandem repeat map highlights multiallelic variants underlying gene expression and agronomic traits in rice," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    5. Sarah A. Mueller & Justin Merondun & Sonja Lečić & Jochen B. W. Wolf, 2025. "Epigenetic variation in light of population genetic practice," Nature Communications, Nature, vol. 16(1), pages 1-14, December.
    6. José Cerca & Bent Petersen & José Miguel Lazaro-Guevara & Angel Rivera-Colón & Siri Birkeland & Joel Vizueta & Siyu Li & Qionghou Li & João Loureiro & Chatchai Kosawang & Patricia Jaramillo Díaz & Gon, 2022. "The genomic basis of the plant island syndrome in Darwin’s giant daisies," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    7. Qianjin Liang & Liyu Chen & Xia Yang & Hui Yang & Shulin Liu & Kun Kou & Lei Fan & Zhifang Zhang & Zongbiao Duan & Yaqin Yuan & Shan Liang & Yucheng Liu & Xingtong Lu & Guoan Zhou & Min Zhang & Fanjia, 2022. "Natural variation of Dt2 determines branching in soybean," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
    8. Hui Shi & Junjie Yin & Zhangjie Zhao & Hong Yu & Hong Yi & Li Xu & Huimin Tong & Min He & Xiaobo Zhu & Xiang Lu & Qing Xiong & Weitao Li & Yongyan Tang & Qingqing Hou & Li Song & Long Wang & Xiaoqiong, 2024. "Fine-tuning of IPA1 transactivation activity by E3 ligase IPI7-mediated non-proteolytic K29-ubiquitination during Magnaporthe oryzae infection," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    9. Luchang Ming & Debao Fu & Zhaona Wu & Hu Zhao & Xingbing Xu & Tingting Xu & Xiaohu Xiong & Mu Li & Yi Zheng & Ge Li & Ling Yang & Chunjiao Xia & Rongfang Zhou & Keyan Liao & Qian Yu & Wenqi Chai & Sij, 2023. "Transcriptome-wide association analyses reveal the impact of regulatory variants on rice panicle architecture and causal gene regulatory networks," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    10. Yongjun Fang & Xiaohu Xiao & Jishan Lin & Qiang Lin & Jiang Wang & Kaiye Liu & Zhonghua Li & Jianfeng Xing & Zhenglin Liu & Baiyu Wang & Yiying Qi & Xiangyu Long & Xia Zeng & Yanshi Hu & Jiyan Qi & Yu, 2024. "Pan-genome and phylogenomic analyses highlight Hevea species delineation and rubber trait evolution," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    11. Lunying Wu & Xiaohui Jing & Baolan Zhang & Shoujun Chen & Ran Xu & Penggen Duan & Danni Zou & Shengjian Huang & Tingbo Zhou & Chengcai An & Yuehua Luo & Yunhai Li, 2022. "A natural allele of OsMS1 responds to temperature changes and confers thermosensitive genic male sterility," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    12. Fei Shen & Yajuan Qin & Rui Wang & Xin Huang & Ying Wang & Tiangang Gao & Junna He & Yue Zhou & Yuannian Jiao & Jianhua Wei & Lei Li & Xiaozeng Yang, 2023. "Comparative genomics reveals a unique nitrogen-carbon balance system in Asteraceae," Nature Communications, Nature, vol. 14(1), pages 1-14, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-62641-w. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.